Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
2mft
Class
DNA
Method
NMR
Summary
Solution NMR structure of the d(gggttttgggtgggttttggg) quadruplex in sodium conditions
Reference
Karsisiotis, A.I., Webba da Silva, M.: "Solution NMR structure of the d(GGGTTTTGGGTGGGTTTTGGG) quadruplex in sodium conditions." To be published
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(D+PD), (2+2), UDDU

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=s--s groove=w-n- planarity=0.183 type=other  nts=4 GGGG A.DG1,A.DG14,A.DG10,A.DG19
 2 glyco-bond=-ss- groove=w-n- planarity=0.123 type=planar nts=4 GGGG A.DG2,A.DG13,A.DG9,A.DG20
 3 glyco-bond=-ss- groove=w-n- planarity=0.208 type=other  nts=4 GGGG A.DG3,A.DG12,A.DG8,A.DG21

List of 1 G4-helix [summary · schematics · tetrads · stems · costacks · homepage]

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

Helix#1, 3 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,A.DG14,A.DG10,A.DG19
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG13,A.DG9,A.DG20
 3  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG3,A.DG12,A.DG8,A.DG21
  step#1  mm(<>,outward)  area=11.18 rise=3.12 twist=22.6
  step#2  pm(>>,forward)  area=14.75 rise=3.22 twist=24.5
  strand#1 DNA glyco-bond=s-- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=-ss nts=3 GGG A.DG14,A.DG13,A.DG12
  strand#3 DNA glyco-bond=-ss nts=3 GGG A.DG10,A.DG9,A.DG8
  strand#4 DNA glyco-bond=s-- nts=3 GGG A.DG19,A.DG20,A.DG21

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2 stacking diagrams
 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,A.DG14,A.DG10,A.DG19
2 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG13,A.DG9,A.DG20
step#1 mm(<>,outward) area=11.18 rise=3.12 twist=22.6

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 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG13,A.DG9,A.DG20
3 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG3,A.DG12,A.DG8,A.DG21
step#2 pm(>>,forward) area=14.75 rise=3.22 twist=24.5

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List of 1 G4-stem [summary · schematics · tetrads · helices · costacks · homepage]

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

Stem#1, 3 G-tetrad layers, 3 loops, INTRA-molecular, UDDU, anti-parallel, 3(D+PD), (2+2)

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,A.DG14,A.DG10,A.DG19
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG13,A.DG9,A.DG20
 3  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG3,A.DG12,A.DG8,A.DG21
  step#1  mm(<>,outward)  area=11.18 rise=3.12 twist=22.6
  step#2  pm(>>,forward)  area=14.75 rise=3.22 twist=24.5
  strand#1  U DNA glyco-bond=s-- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  D DNA glyco-bond=-ss nts=3 GGG A.DG14,A.DG13,A.DG12
  strand#3  D DNA glyco-bond=-ss nts=3 GGG A.DG10,A.DG9,A.DG8
  strand#4  U DNA glyco-bond=s-- nts=3 GGG A.DG19,A.DG20,A.DG21
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT A.DT4,A.DT5,A.DT6,A.DT7
  loop#2 type=propeller strands=[#3,#2] nts=1 T A.DT11
  loop#3 type=diagonal  strands=[#2,#4] nts=4 TTTT A.DT15,A.DT16,A.DT17,A.DT18

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 0 non-stem G4-loops (including the two closing Gs)